def test_align_pair_ins_punish_indel(self):
result = align_pair(self._reference, self._reference_rc,
('TTATGACAAGT', 'CGTAACGAGC'), 3)
assert result == ((4, 34), (3, 11))
def test_align_pair_del_punish_indel(self):
result = align_pair(self._reference, self._reference_rc,
('TTATGAAGT', 'CGTAGAGC'), 3)
assert result == ((3, 35), (3, 11))
def test_align_pair_del(self):
result = align_pair(self._reference, self._reference_rc,
('TTATGAAGT', 'CGTAGAGC'))
assert result == ((2, 34), (1, 11))
def test_align_pair_ins(self):
result = align_pair(self._reference, self._reference_rc,
('TTATGACAAGT', 'CGTAACGAGC'))
assert result == ((3, 43), (1, 11))
def test_align_pair_perfect(self):
result = align_pair(self._reference, self._reference_rc,
('TTATGAAAGT', 'CGTAAGAGC'))
assert result == ((3, 34), (0, 11))